Ugo, I always line up off the runways. The stock aprons and taxiways in FSX can be anywhere from close to not close to some not even there. With Island airports, you'll even find that the stock land mass sometimes doesn't match up with the real thing. Always start off the runways and work from there.

Jim, I'd defenitely state that unless you plan on moving the runway and all the underlying hassle that comes with it (having to completely redo approach code, etc.), that lining up on the main runway and designing off that is the best way to go.

I always match the bacground image's runway to the one in ADE and then design the rest of the airport, moving taxiways, aprons, etc. to match my image.

Jim, I prefer to use a good airport Chart, but have also used
Google Earth and other images when Jepp Charts aren't
available.

The airport chart is usually my main background image and the
one I line the runway up from, but I also use other
photographic type images and switch them on and off for
reference when designing. Sometimes it's even beneficial to
take a screenshot in FSX and have it as a background image. It
may seem redundant, but it can help with knowing where land
features are (such as the edge of an island, etc).

EDIT: Here is a screenshot I took back when I was starting
TKXF showing the layering of the Airport Chart and a FSX
Screenshot. It also shows the Chart as the first background
image lined up on the runway. Notice how the land does not
line up with the airport chart and hence, you have to
compromise on accuracy when designing the rest of the airport
( unless you want to mess with shorelines ).

EDIT#2:Added a thumbnail since the original image is wide for the forums. Click the picture to see it original size.